6DFH

BG505 MD64 N332-GT2 SOSIP trimer in complex with germline-reverted BG18 fragment antigen binding

• PDB DOI: https://doi.org/10.2210/pdb6DFH/pdb
• EM Map EMD-7876: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2018-05-14 Released: 2019-11-06 
• Deposition Author(s): Ozorowski, G., Steichen, J.M., Schief, W.R., Ward, A.B.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 12-mer - A6B3C3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 375.57 kDa 
• Atom Count: 20,046 
• Modelled Residue Count: 2,406 
• Deposited Residue Count: 3,255 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	A, E [auth C], I [auth D]	476	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Explore Q2N0S6  Go to UniProtKB:  Q2N0S6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	B, F [auth E], J [auth F]	162	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus 1) Explore Q2N0S5  Go to UniProtKB:  Q2N0S5

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
germline-reverted BG18 fragment antigen binding heavy chain	C [auth H], G, K [auth I]	233	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
germline-reverted BG18 fragment antigen binding light chain	D [auth L], H [auth J], L [auth K]	214	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], JA [auth j], M, N, O, P, Q, T, U, V, W, X, Y	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	HA [auth h], R, Z	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42227JK GlyCosmos:  G42227JK GlyGen:  G42227JK

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], IA [auth i], S	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G46836GH GlyCosmos:  G46836GH GlyGen:  G46836GH

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AB [auth D], BB [auth F], KA [auth A], LA [auth A], MA [auth A], NA [auth A], OA [auth A], PA [auth B], QA [auth C], RA [auth C], SA [auth C], TA [auth C], UA [auth C], VA [auth E], WA [auth D], XA [auth D], YA [auth D], ZA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.1
MODEL REFINEMENT	PHENIX	1.12
MODEL REFINEMENT	Coot	0.8.9

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-11-06 
Deposition Author(s): Ozorowski, G., Steichen, J.M., Schief, W.R., Ward, A.B.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1 AI100663
Bill & Melinda Gates Foundation	United States	OPP1115782
Bill & Melinda Gates Foundation	United States	OPP1084519

Revision History  

• Version 1.0: 2019-11-06
  Type: Initial release
  
• Version 1.1: 2019-11-13
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence, Database references, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary